Horse coat colors look endlessly varied, but most of them come from a small number of genes acting on two pigments. Once you know which gene does what, a palomino, a buckskin, a grulla or a blue roan stops being a mystery and becomes a predictable combination. This is also why color DNA tests are among the most widely used tests in horse breeding: they tell you what a horse carries, not just what it shows, and so what it can pass to a foal.
Key facts
- Every coat starts from two pigments: black/brown eumelanin and red/yellow pheomelanin.
- Two genes set the base color: Extension (MC1R) decides whether black pigment can be made, and Agouti (ASIP) decides where it goes. Together they give chestnut, bay and black.
- Dilution genes (cream, dun, silver, champagne, pearl) lighten the base color; gray (STX17) turns any color white with age.
- White patterns such as tobiano (KIT) and frame overo (EDNRB) are separate genes; two copies of frame overo cause lethal white foal syndrome.
Two pigments, three base colors
Melanocytes in the hair follicles make either eumelanin (black or brown) or pheomelanin (red or yellow). Which one they make is controlled first by the Extension gene, MC1R, the melanocortin 1 receptor. The dominant form, written E, allows black pigment. A horse with two copies of the recessive e form cannot make black pigment in its coat and is chestnut (sorrel in some breeds), whatever else it carries. This was one of the first coat color genes mapped in horses, by Marklund and colleagues in 1996.
In a horse that can make black pigment, the Agouti gene, ASIP, decides where it goes. The dominant A form restricts black to the "points" (mane, tail, lower legs and ear rims), giving a bay. A horse with two copies of the recessive a form has black pigment all over and is black. Agouti has no visible effect on a chestnut, because there is no black pigment for it to move, which is why two chestnuts can sometimes surprise a breeder by carrying agouti alleles they never showed.
| Extension | Agouti | Base color |
|---|---|---|
| ee | any | Chestnut |
| E_ | A_ | Bay |
| E_ | aa | Black |
The underscore means the second copy can be either form. Shades such as seal brown, liver chestnut or blood bay come from other, less well understood genetic and environmental factors.
Dilution genes
Cream (SLC45A2)
Cream is incompletely dominant, so one copy and two copies look different. One copy lightens red pigment to gold but leaves black almost untouched: a chestnut becomes a palomino, a bay becomes a buckskin and a black becomes a smoky black, which can be hard to tell from an ordinary black without a test. Two copies dilute both pigments to cream, with pink skin and blue eyes: cremello (on chestnut), perlino (on bay) and smoky cream (on black).
Dun (TBX3)
Dun is dominant. It lightens the body while leaving the head, legs and a dorsal stripe darker, and it often adds leg barring and shoulder stripes, the so-called primitive markings. A bay dun is the classic yellow dun, a black dun is a grulla, and a chestnut dun is a red dun. Imsland and colleagues showed in 2016 that dun works by depositing pigment unevenly around each hair, controlled by the TBX3 gene, and that the non-dun state in most horses is caused by regulatory changes near that gene (Nature Genetics 48:152–158).
Silver (PMEL17)
Silver dilutes black pigment only, so it shows on black and bay horses and is invisible on chestnuts. Black silvers have a chocolate body with a flaxen mane and tail. The same variant is associated with multiple congenital ocular anomalies (MCOA), so breeders of silver horses often have the eyes examined.
Champagne and pearl
Champagne (SLC36A1) dilutes both pigments and gives mottled pinkish skin and amber eyes. Pearl is a variant of the same gene as cream; it has little visible effect on its own but produces a cream-like dilution when combined with a cream allele or a second pearl allele.
Gray
A gray horse is born colored and loses pigment from its hair year by year until it is white or "flea-bitten". Gray is dominant and acts on any base color, so a gray horse's original color is often only visible in foal photos. Rosengren Pielberg and colleagues identified the cause in 2008: a 4.6-kilobase duplication in intron 6 of the STX17 gene (Nature Genetics 40:1004–1009). The same mutation makes gray horses prone to melanoma, which is very common in older grays, so owners are advised to have skin lumps under the tail and around the anus checked by a veterinarian.
White patterns
White markings and spotting come from genes that affect how pigment cells migrate in the embryo. White patterning is the largest group of color genes in horses. A few of the best known:
- Tobiano (KIT): dominant, typically white crossing the back, with white legs and a dark head. It is caused by a large chromosomal inversion near the KIT gene (Brooks et al., 2007).
- Frame overo (EDNRB): irregular, mostly horizontal white patches on the sides and neck. One copy gives the pattern. Two copies cause overo lethal white syndrome: the foal is born nearly all white with a non-functioning gut and does not survive. Testing before breeding two frame carriers avoids it.
- Splashed white (MITF and PAX3 variants): white legs and belly with a "dipped in paint" look and often blue eyes; some forms are linked to deafness.
- Sabino-1 (KIT): roaned, ragged white edges, with extensive white in horses that carry two copies.
- Leopard complex (TRPM1): the spotted patterns of the Appaloosa and Knabstrupper. Horses with two copies are at risk of congenital stationary night blindness.
- Roan: white hairs mixed through the body coat with a solid head and legs, linked to the KIT region.
What a color DNA test tells you
A color test reports the alleles a horse carries at each tested gene. That answers questions the eye cannot: is this black horse a smoky black carrying cream, does this chestnut carry agouti, can these two horses produce a chestnut or a lethal white foal. Breed registries also use color tests to confirm registration papers. Most laboratories need a mane or tail hair sample with the roots attached, or a blood sample taken by a veterinarian.
Two cautions. First, not every pattern has a known gene. Many horses with white markings or unusual patterns carry variants that no test yet detects, so a negative result does not always explain what you see. Second, some color variants are tied to health effects (gray and melanoma, silver and eye anomalies, frame overo and lethal white, leopard complex and night blindness), so a color test is also a health tool for breeders.
Horse parentage testing was historically one of the services described on the Genoscoper horse tests page; for current tests, contact an accredited equine genetics laboratory.
Frequently asked questions
Can two chestnut horses have a bay foal?
No. Chestnuts are ee at Extension and can only pass on e, so a foal of two chestnuts is always chestnut-based (it can still be diluted or patterned, for example palomino if a parent carries cream). Apparent exceptions usually turn out to be a misidentified color or wrong parentage.
What is the difference between a buckskin and a dun?
Both can look tan with black points, but buckskin is a bay with one cream allele, while dun is a separate gene that adds a dorsal stripe and often leg barring. A DNA test separates them reliably.
Why do gray horses turn white?
The STX17 duplication causes the pigment cells in the hair follicles to wear out early, so each new coat carries less pigment. The skin usually stays dark.
Is lethal white foal syndrome preventable?
Yes. It only occurs when a foal inherits frame overo from both parents. Testing breeding horses and not mating two carriers prevents it.
Sources
- Marklund L, et al. (1996). A missense mutation in the gene for melanocyte-stimulating hormone receptor (MC1R) is associated with the chestnut coat color in horses. Mammalian Genome 7:895–899.
- Imsland F, et al. (2016). Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation that underlies Dun camouflage color in horses. Nature Genetics 48:152–158. doi:10.1038/ng.3475.
- Rosengren Pielberg G, et al. (2008). A cis-acting regulatory mutation causes premature hair graying and susceptibility to melanoma in the horse. Nature Genetics 40:1004–1009. doi:10.1038/ng.185.
- Brooks SA, et al. (2007). A chromosome inversion near the KIT gene and the Tobiano spotting pattern in horses. Cytogenetic and Genome Research 119:225–230.
- Metallinos DL, Bowling AT, Rine J (1998). A missense mutation in the endothelin-B receptor gene is associated with Lethal White Foal Syndrome. Mammalian Genome 9:426–431.
- OMIA, University of Sydney: Online Mendelian Inheritance in Animals (horse coat color entries).